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Elife. 2018 Feb 9;7. pii: e31486. doi: 10.7554/eLife.31486.

Pi-Pi contacts are an overlooked protein feature relevant to phase separation.

Author information

1
Program in Molecular Medicine, Hospital for Sick Children, Toronto, Canada.
2
Department of Biochemistry, University of Toronto, Toronto, Canada.

Abstract

Protein phase separation is implicated in formation of membraneless organelles, signaling puncta and the nuclear pore. Multivalent interactions of modular binding domains and their target motifs can drive phase separation. However, forces promoting the more common phase separation of intrinsically disordered regions are less understood, with suggested roles for multivalent cation-pi, pi-pi, and charge interactions and the hydrophobic effect. Known phase-separating proteins are enriched in pi-orbital containing residues and thus we analyzed pi-interactions in folded proteins. We found that pi-pi interactions involving non-aromatic groups are widespread, underestimated by force-fields used in structure calculations and correlated with solvation and lack of regular secondary structure, properties associated with disordered regions. We present a phase separation predictive algorithm based on pi interaction frequency, highlighting proteins involved in biomaterials and RNA processing.

KEYWORDS:

bioinformatics; computational biology; human; molecular biophysics; pi interactions; prediction; protein interactions; protein phase separation; protein structure; structural biology; systems biology

PMID:
29424691
PMCID:
PMC5847340
DOI:
10.7554/eLife.31486
[Indexed for MEDLINE]
Free PMC Article

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